The blood–brain barrier is formed by the brain capillary endothelium and plays a neuroprotective role in healthy brain function. For researchers studying gene expression within the central nervous system vasculature, endothelial heterogeneity can pose a challenge. Whole tissue samples—homogenates of brain and or spinal cord, for example—are composed of multiple endothelial cell types from different regions of the CNS, resulting in a pooling of cells and an unclear characterization of endothelial cell subtypes.